Erik,
I'm afraid that you will not be able to fold your RNA on mulfold. Even if
you patch sequences together, it will not necessarily reflect the natural
case because, as you suspect, distant sequences can interact with each
other, and unless they are all represented in one fold you will not be able
to see all possible interactions. You may "miss" the _most_
thermodynamically stable structure. I suppose it may be possible to fold
segments of it and try to extrapolate a full structure by doing some serious
foldings, but this would certainly take a lot of time and cleverness on your
part, and, in the end, you still won't know how much of it you can trust.
There are some cases in E coli where it is believed that 3' sequences in an
mRNA fold back to pair with the SD sequence and thus block ribosome binding
(see Thisted et al, (94) EMBO: 13(8):1950-59). You mentioned your RNA is
~4000 bases but not if it is eukaryotic or prokaryotic. This could be
significant because translation and transcription are coupled in E coli and
this could shorten the window of opportunity for distal sequences to
interact. This effect should be directly related to the distance between
complementary sequences and strength of the SD sequence (competition with
ribosome binding).
The mulfold that I have been using is from the GCG package. I don't know if
it is the same as the one you mention. We can use it with Mac or IBM. In
either case it will not fold very long sequences. I hope this was somewhat
helpful.
Good luck,
Brian Zeiler
brianz at microbio.lifesci.ucla.edu